bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.10.15.759361

Chromosome-level genome assembly of Falcataria falcata provides insights into ancient polyploidy and duplicate gene evolution in Fabaceae

Kobayashi, M. J.·Chigira, O.·Widiyatno, W.·Na'iem, M.·Tani, N.
View original source ↗Export metadata ↓

Abstract

Whole-genome duplication (WGD) has played a fundamental role in shaping plant genome evolution, yet the timing and independence of WGD events in major Fabaceae subfamilies, including Caesalpinioideae and Papilionoideae, remain debated. Here, we present a chromosome-level genome assembly of the tropical mimosoid tree Falcataria falcata within Caesalpinioideae and investigate the evolutionary consequences of ancient polyploidy. The assembled genome spans 614.9 Mb with 13 chromosome-level scaffolds and 99.6% completeness based on BUSCO assessment, providing a high-quality resource for comparative genomics. Synteny analyses revealed conserved macrosyntenic structures shared across Caesalpinioideae, consistent with an ancestral WGD event predating lineage diversification. In contrast, analyses of synonymous substitution rates (Ks) and phylogenetic relationships of conserved duplicate genes support independent WGD events in Caesalpinioideae and Papilionoideae. We further show that lineage-specific variation in synonymous substitution rates is negatively associated with the retention of WGD-derived duplicates following the ancestral WGD in Caesalpinioideae, suggesting that evolutionary rate heterogeneity plays a key role in post-WGD genome evolution. In addition, recent gene duplicates that arose independently in each lineage after WGD exhibit elevated Ka/Ks ratios and are predominantly associated with defense responses to diverse biotic stresses, suggesting more rapid sequence evolution and functional divergence compared with WGD-derived duplicates. Together, our results reveal how ancient WGD, lineage-specific evolutionary rates, and subsequent gene duplication have jointly structured genome evolution in Fabaceae. The genome of F. falcata provides a valuable resource for understanding the long-term evolutionary consequences of polyploidy and the diversification of ecological adaptations in legumes.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Kobayashi, M. J., Chigira, O., Widiyatno, W., Na'iem, M., Tani, N.. 2026-10-16. Chromosome-level genome assembly of Falcataria falcata provides insights into ancient polyploidy and duplicate gene evolution in Fabaceae. https://doi.org/10.64898/2026.10.15.759361

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrated Multiomics Reveals Intergenerational Brain Sensory System Remodeling Induced by Parental Intermittent Fasting

Intermittent fasting (IF) is increasingly recognized as a potent modulator of metabolic health, but its effects on brain function across generations remain poorly understood. Here, we show that parental IF, administered to both mothers and fathers before mating, is associated with coordinated molecular remodeling in the cerebral cortex of fathers and their offspring, with shared molecular signatures identified between these generations and a pronounced enrichment of sensory-associated pathways. Using whole-genome bisulfite sequencing, transcriptomic profiling, and proteomic analysis, we found that IF elicited widespread cortical epigenetic remodeling in fathers, accompanied by transcriptional and protein-level changes enriched for olfactory, taste, synaptic, and neurometabolic pathways. Strikingly, related molecular signatures were detected in F1 offspring that had never been directly exposed to fasting, consistent with intergenerational transmission of IF-associated cortical remodeling. Offspring responses were sex dependent, with female and male progeny exhibiting distinct patterns of DNA methylation, gene expression, and protein abundance. Integrated multiomic analyses identified conserved candidate networks involved in sensory perception, glutamatergic signaling, synaptic organization, intracellular trafficking, cytoskeletal regulation, and stress-response pathways. Together, these findings identify sensory-associated cortical remodeling as a prominent molecular feature associated with parental IF and reveal persistent, sex-dependent molecular alterations in the offspring brain.

genomics↗
bioRxiv2026

RegDesign-Bench: Benchmarking computational methods for cell-type-specific regulatory DNA design

The de novo design of regulatory DNA sequences that drive cell-type-specific gene expression could enable precise gene control in synthetic biology, cell engineering and gene therapy. Various computational methods have been developed for this task, yet systematic comparisons that guide method selection for different design objectives remain limited. Here, we introduce RegDesign-Bench, a standardized framework for evaluating cell-type-specific cis-regulatory element design through a comprehensive set of computational analyses. Among the methods tested, strong predicted activity was not consistently accompanied by cell-type-selective accessibility or prominent cell-type-associated motif signals. Similarity to reference sequence distributions also did not ensure high predicted target-cell activity or specificity. These findings demonstrate that favourable performance on individual measurements does not necessarily extend across regulatory properties and library characteristics, revealing application-dependent strengths and limitations of current design methods. Overall, RegDesign-Bench offers a general-purpose computational framework for comparing and selecting methods to design regulatory DNA that drives cell-type-specific gene expression.

genomics↗
bioRxiv2026

Thille, a chromosome-level type B avocado genome, and the structural and allelic variation at candidate flowering-type loci

Avocado (Persea americana Mill.) is heterodichogamous: each flower opens first as female and then as male, and cultivars fall into two complementary flowering types, A and B, determined by the transcription factor SDMYB, whose dominant allele confers type A. Avocado genomes have so far come from type A cultivars. Here we report a chromosome-level genome of Thille, a type B cultivar used in breeding. From 72.2 Gb of PacBio HiFi reads (81x coverage) and Omni-C data, the assembly places 859.8 Mb, 96% of the expected 896 Mb genome, in 12 chromosomes with an NG50 of 84.5 Mb, a consensus quality of QV 69.95, and 97.3% complete BUSCO genes; repeats occupy 64.0% of the assembly, and 35,386 protein-coding genes were predicted. We compared Thille with the type A cultivars Hass and Puebla, a predominantly Guatemalan hybrid, and with a West Indian (WI) accession, a Lowland botanical group variety of unreported flowering type. The assemblies differ by large rearrangements, including an 18.8 Mb inversion on chromosome 12 specific to Hass. Using phased reads and haplotype assemblies, we reconstructed the alleles of candidate flowering genes from a type A versus type B Fst scan. Both WI haplotypes carry the recessive SDMYB allele found in Thille; based on this study and the previous study of SDMYB, we predict the WI accession to be type B. Six genes, including SDMYB, carry an allele shared by all three type A cultivars and absent from Thille and WI. The genome and HiFi reads are available under BioProject PRJNA1142556.

genomics↗